Model Internals

Each PhenDB model is trained on sets of bacterial ENOGs (orthologous groups from EggNOG 4.5), which have or have not been identified in the training genomes. Each ENOG is given a weight, with the magnitude of the weight being the importance of that ENOG for the final prediction. The sign of the weight indicates whether the presence (positive weight) or absence (negative weight) of this ENOG is indicative of the trait.

This table lists the 250 highest-ranking ENOGs of this model.

rank in model enog name enog description weight in model
1 ENOG4108E16 pectate lyase 0.013865
2 ENOG4106UHK Pfam:DspF 0.013371
3 ENOG4106NSY Pathogenicity factor 0.013345
4 ENOG410712N HrpF protein 0.006373
4 ENOG4106Y4G Type III secretion apparatus protein, YscI HrpB family 0.006373
5 ENOG4108DKF FHIPEP family 0.012384
6 ENOG4105H8R type iii secretion 0.012144
7 ENOG4106VVZ type iii secretion 0.002373
7 ENOG41065ZF type iii secretion 0.002373
7 ENOG41067UE type iii secretion 0.002373
7 ENOG4107DRV type iii secretion protein 0.002373
7 ENOG4108SJN type iii secretion protein 0.002373
8 ENOG4108TN6 type iii secretion 0.002962
8 ENOG4107Y59 type iii secretion 0.002962
8 ENOG4105K44 type iii secretion 0.002962
8 ENOG4108HHI Type III secretion system protein 0.002962
9 ENOG41071F5 type iii secretion 0.011785
10 ENOG4106ZDQ NA 0.011650
11 ENOG4106YFX HrpW-specific chaperone 0.011350
12 ENOG4107XGZ Hydrolase -0.010869
13 ENOG410631C RNA polymerase 0.005428
13 ENOG41074M8 Major structure protein of the hrp pilus, which is a component of the type III secretion system (TTSS, Hrp secretion system) required for effector protein delivery, parasitism, and pathogenicity. The hrp pilus functions as a conduit for protein delivery into the host cell (By similarity) 0.005428
14 ENOG4107362 NA 0.005385
14 ENOG41072RG type iii secretion protein 0.005385
15 ENOG4108Y78 type iii secretion 0.010495
16 ENOG4108XQD Bacterial regulatory protein, Fis family 0.005205
16 ENOG41076DT NA 0.005205
17 ENOG4106KKT HrpZ 0.009895
18 ENOG4108NN2 NA -0.009818
19 ENOG4105M1F (LipO)protein 0.009741
20 ENOG4108S3Z Histidine kinase 0.004799
20 ENOG4108U56 two component transcriptional regulator, LuxR family 0.004799
21 ENOG4105V4E HTH_XRE 0.009404
22 ENOG4105ZN9 NA 0.009025
23 ENOG4105PZD NA 0.008502
24 ENOG4108PVD exported protein -0.008101
25 ENOG4105RHY Pfam:UPF0157 -0.007993
26 ENOG4108WHK AraC Family Transcriptional Regulator -0.007926
27 ENOG4105QEP PRD domain protein -0.003957
27 ENOG4105FNR Membrane -0.003957
28 ENOG4107ZD0 death ON curing protein 0.007865
29 ENOG4106DTN NA 0.007776
30 ENOG4108TFY Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate (By similarity) -0.007769
31 ENOG4105H5R lysr family transcriptional regulator -0.003869
31 ENOG4107RNN dihydropyrimidinase (EC 3.5.2.2) -0.003869
32 ENOG4105KVH Transcriptional regulator 0.007698
33 ENOG4107QK5 Homocysteine s-methyltransferase 0.007559
34 ENOG4105YEH PAAR repeat-containing protein 0.007492
35 ENOG4107HW9 Pfam:TonB 0.001873
35 ENOG4107YU0 Glycerophosphoryl diester phosphodiesterase family 0.001873
35 ENOG4106MV0 NA 0.001873
35 ENOG4108WET LysR family transcriptional Regulator 0.001873
36 ENOG4105F1Y L-lysine 6-monooxygenase (NADPH) -0.007373
37 ENOG4105NRD DNA-damage-inducible protein J 0.007364
38 ENOG4105KBY Plasmid stabilization system protein 0.007364
39 ENOG4105UQ8 TrbM 0.002447
39 ENOG4108XQC type IV secretion system protein VirB10 0.002447
39 ENOG4105NT4 type IV secretion system protein VirB1 0.002447
40 ENOG4108IUP Binding-protein-dependent transport systems, inner membrane component 0.007331
41 ENOG4108KHX Diguanylate cyclase -0.007330
42 ENOG4108EIY Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM), which serves as an aminopropyl donor (By similarity) 0.007305
43 ENOG4105DH8 myo-inositol catabolism 0.007258
44 ENOG4108Z0A Cupin 2, conserved barrel domain protein 0.007240
45 ENOG4108ZUS Transcriptional regulator -0.001028
45 ENOG41069H0 dihydroorotase EC 3.5.2.3 -0.001028
45 ENOG4107QHH Pyridoxal phosphate-dependent enzyme -0.001028
45 ENOG4108SI9 PRD domain protein -0.001028
45 ENOG4105DYE Membrane -0.001028
45 ENOG4106013 cytoplasmic protein -0.001028
45 ENOG4105CI9 4-hydroxy-2-oxoglutarate aldolase -0.001028
46 ENOG4108DIN LysR family Transcriptional regulator 0.007161
47 ENOG4105QY9 Beta-lactamase 0.007121
48 ENOG4107SH8 TPR repeat-containing protein 0.007113
49 ENOG4105MPC Transcriptional regulator 0.002371
49 ENOG4108KCE plasmid partition ParA protein 0.002371
49 ENOG4108SJ2 short-chain dehydrogenase reductase 0.002371
50 ENOG4105DZI LysR family Transcriptional regulator -0.007078
51 ENOG4108WRP synthetase -0.007016
52 ENOG4108IHU transport system permease protein 0.007007
53 ENOG4108IJ8 ABC transporter -0.006962
54 ENOG41085PU Protein of unknown function (DUF2384) 0.006951
55 ENOG4105MS1 LysR family transcriptional Regulator 0.006917
56 ENOG4108URH decarboxylase -0.006917
57 ENOG4107RY4 Alcohol dehydrogenase GroES-like domain 0.006884
58 ENOG4105VDQ RES domain-containing protein 0.006865
59 ENOG41069X8 NA -0.003422
59 ENOG4105WPU NA -0.003422
60 ENOG4107RGH Aldehyde dehydrogenase 0.006842
61 ENOG4106M69 NA 0.006827
62 ENOG4105FDS Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine (By similarity) 0.006753
63 ENOG4108Q9V regulatoR -0.006668
64 ENOG4107X5A tonB-dependent Receptor 0.006583
65 ENOG4105H55 gCN5-related N-acetyltransferase -0.006564
66 ENOG4108Z7T Destroys radicals which are normally produced within the cells and which are toxic to biological systems (By similarity) 0.006552
67 ENOG4105NRM Membrane -0.006529
68 ENOG4108V87 frv operon regulatory protein -0.006455
69 ENOG4105EJB Short-chain dehydrogenase reductase Sdr -0.006455
70 ENOG4107288 Membrane -0.006444
71 ENOG4108J5K non-ribosomal peptide synthetase 0.006420
72 ENOG4108KBE Glycosyl transferase, family 2 0.006418
73 ENOG41077RS Phosphatase -0.001280
73 ENOG4108UMZ Cdp-alcohol phosphatidyltransferase -0.001280
73 ENOG4107TVY Phosphatidate cytidylyltransferase -0.001280
73 ENOG4108RX3 Acyl-transferase -0.001280
73 ENOG4107XTH Alpha Beta Hydrolase Fold protein -0.001280
74 ENOG4105PDG Type IV secretion system protein VirB8 0.006386
75 ENOG4105ZDF NA -0.006379
76 ENOG4107V9I sulfatase-modifying factor protein -0.006379
77 ENOG4105D78 K07001 NTE family protein -0.006373
78 ENOG4108EPX Catalyzes the last two steps in the biosynthesis of 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity) -0.006368
79 ENOG4105CWG Catalyzes the last two steps in the biosynthesis of 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity) 0.006368
80 ENOG4108KM4 amino acid AbC transporter 0.001592
80 ENOG4108Q2S LysR family transcriptional regulator 0.001592
80 ENOG4108K31 extracellular solute-binding protein 0.001592
80 ENOG4107SSX brancheD-chain amino acid aminotransferase 0.001592
81 ENOG4109025 Glyoxalase Bleomycin resistance protein (Dioxygenase 0.006329
82 ENOG4105CPZ Transcriptional regulator, rpir family 0.006299
83 ENOG4108MES Periplasmic binding protein 0.006287
84 ENOG4107Z72 Siderophore biosynthesis protein -0.006267
85 ENOG4108EIA ABC-type transporter, periplasmic subunit 0.006243
86 ENOG410634P phospholipase d 0.006221
87 ENOG4108UZ9 MotA TolQ exbB proton channel 0.002074
87 ENOG4108ZJQ Biopolymer transport protein exbD tolR 0.002074
87 ENOG4105IKD Pfam:TonB 0.002074
88 ENOG4108KD5 ADP-ribosylation crystallin J1 -0.003109
88 ENOG4108TFM Kinase, PfkB family -0.003109
89 ENOG4105FDP GntR family transcriptional regulator -0.006211
90 ENOG4105CSN Binding-protein-dependent transport systems, inner membrane component 0.006203
91 ENOG4105PUE CRISPR-associated protein, Cse2 family -0.006194
92 ENOG4105ZQY transcriptional regulator -0.006190
93 ENOG410887A amino acid ABC transporter -0.003091
93 ENOG4105MSC amino acid AbC transporter -0.003091
94 ENOG4107QMY polysaccharide deacetylase -0.003068
94 ENOG4108K08 polysaccharide deacetylase -0.003068
95 ENOG4105EPE integral membrane protein 0.006128
96 ENOG4105MRF Integrase -0.006127
97 ENOG4105EP3 fad dependent oxidoreductase 0.006122
98 ENOG4107UIH DeoR-like helix-turn-helix domain 0.006121
99 ENOG4106NV4 (ABC) transporter -0.000764
99 ENOG4108QM5 GntR Family Transcriptional Regulator -0.000764
99 ENOG41071G1 Uncharacterized protein YceQ -0.000764
99 ENOG41083U6 Inherit from COG: PAAR repeat-containing protein -0.000764
99 ENOG41069DZ NA -0.000764
99 ENOG4108T01 NA -0.000764
99 ENOG4105SSR PTS System -0.000764
99 ENOG4105D4B ABC, transporter -0.000764
100 ENOG41080IT Antibiotic biosynthesis monooxygenase -0.006112
101 ENOG4105VI0 Pts system, glucitol sorbitol-specific -0.006089
102 ENOG4105H9A dihydrodipicolinate -0.006073
103 ENOG4105KJ6 Lysine exporter protein (Lyse ygga) 0.006066
104 ENOG4107R6G Catalyzes the S-adenosylmethionine monomethyl esterification of trans-aconitate (By similarity) -0.006065
105 ENOG4105CH6 catalase 0.006050
106 ENOG4108MCV Uncharacterized alpha/beta hydrolase domain (DUF2235) 0.006033
107 ENOG4105HJ4 Major pilin protein fimA -0.005999
108 ENOG4108K8R Glutathione S-transferase -0.005989
109 ENOG4108MY7 Fimbrial 0.005981
110 ENOG4108MHR Repressor involved in choline regulation of the bet genes (By similarity) 0.005971
111 ENOG4108NYH LysR family Transcriptional regulator 0.005916
112 ENOG41076MN Phosphoesterase, PA-phosphatase related -0.005911
113 ENOG4106WCH Major Facilitator superfamily 0.005885
114 ENOG4108HKT sucrose-6-phosphate hydrolase 0.005866
115 ENOG4105DE9 3-keto-5-aminohexanoate cleavage enzyme -0.005864
116 ENOG4108Z6N Transcriptional regulator, ARAC family -0.005843
117 ENOG4105PAD Hydrolase 0.005833
118 ENOG4105DZK receptor 0.005811
119 ENOG4108REG Glutathione S-transferase 0.005810
120 ENOG41090BE (LipO)protein 0.005800
121 ENOG4105JKQ Part of the ABC transporter complex BtuCDF involved in vitamin B12 import. Binds vitamin B12 and delivers it to the periplasmic surface of BtuC (By similarity) -0.002896
121 ENOG4105VS7 Bifunctional enzyme which can phosphorylate or dephosphorylate isocitrate dehydrogenase (IDH) on a specific serine residue. This is a regulatory mechanism which enables bacteria to bypass the Krebs cycle via the glyoxylate shunt in response to the source of carbon. When bacteria are grown on glucose, IDH is fully active and unphosphorylated, but when grown on acetate or ethanol, the activity of IDH declines drastically concomitant with its phosphorylation (By similarity) -0.002896
122 ENOG4107QTC Aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding -0.002890
122 ENOG4107XKX isoquinoline 1-oxidoreductase, alpha subunit -0.002890
123 ENOG4105X6N Stress-induced bacterial acidophilic repeat motif -0.005778
124 ENOG4108ZFX Mannosyl-3-phosphoglycerate phosphatase 0.001924
124 ENOG410801S Inherit from COG: Glycosyl transferase, family 2 0.001924
124 ENOG4105YP7 UPF0270 protein 0.001924
125 ENOG4105IGJ Zn-dependent Hydrolase of the beta-lactamase fold protein 0.005767
126 ENOG4108ZHR arsR family transcriptional regulator -0.005756
127 ENOG4108V0P LemA family -0.005754
128 ENOG4107RCV ABC transporter, permease -0.002862
128 ENOG4105C4Y ABC transporter -0.002862
129 ENOG4108KSI GntR Family Transcriptional Regulator 0.005721
130 ENOG4108JQW Xylose isomerase-like TIM barrel 0.005714
131 ENOG4108MQR type VI secretion-associated protein, ImpA family -0.002852
131 ENOG4106BVW Protein of unknown function (DUF877) -0.002852
132 ENOG4105EJC lysr family transcriptional regulator -0.005693
133 ENOG4108QK1 type VI secretion system, lysozyme-related protein -0.005688
134 ENOG4108URP Dtdp-4-dehydrorhamnose 3,5-epimerase -0.002842
134 ENOG4105DBZ Dtdp-4-dehydrorhamnose reductase -0.002842
135 ENOG4108EZF protein-Npi-phosphohistidine-sugar phosphotransferase (EC 2.7.1.69) -0.005679
136 ENOG4108IPX Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system (By similarity) -0.005668
137 ENOG4105RIH Conjugal transfer protein 0.000515
137 ENOG41083C4 MA 0.000515
137 ENOG4107I1F NA 0.000515
137 ENOG4108DKI Pfam:GSPII_E 0.000515
137 ENOG4108DKJ flavin oxidoreductase 0.000515
137 ENOG4107JAW Type IV secretion system proteins 0.000515
137 ENOG4105TCU NA 0.000515
137 ENOG410629I TriK protein 0.000515
137 ENOG4108PCE TRANSFER protein 0.000515
137 ENOG4108MH9 Conjugal transfer protein 0.000515
137 ENOG4106GYY NA 0.000515
138 ENOG4105KS6 transposase -0.005659
139 ENOG4107SJI Dehydrogenase -0.005644
140 ENOG4108ZXT Transcriptional regulator 0.005629
141 ENOG4105NW4 Pfam:PhdYeFM 0.005622
142 ENOG4105G3H inositol mono-phosphatase -0.005607
143 ENOG4105NRA 50s ribosomal protein l31 type b 0.005601
144 ENOG4108JIK carboxylase -0.005590
145 ENOG4105XW1 ANK 0.005587
146 ENOG4107BVJ 4,5-dihydroxyphthalate decarboxylase -0.000294
146 ENOG4106YFW NA -0.000294
146 ENOG4105ISK RES domain-containing protein -0.000294
146 ENOG4105XQ9 regulatory protein -0.000294
146 ENOG4108EQA pts system -0.000294
146 ENOG4105YJC Repressor protein -0.000294
146 ENOG4105CSW GntR family transcriptional regulator -0.000294
146 ENOG4107RCU alcohol dehydrogenase -0.000294
146 ENOG4107Y62 Transcriptional regulator, TetR family -0.000294
146 ENOG4105CPN adenine deaminase -0.000294
146 ENOG4108SUN Protein of unknown function (DUF2848) -0.000294
146 ENOG4105K2J Transcriptional regulator -0.000294
146 ENOG4107QQ7 Outer membrane porin -0.000294
146 ENOG4108TDU NA -0.000294
146 ENOG4106G52 NA -0.000294
146 ENOG4105EQ6 Hydrolyzes dipeptides containing N-terminal aspartate residues. May play a role in allowing the cell to use peptide aspartate to spare carbon otherwise required for the synthesis of the aspartate family of amino acids (By similarity) -0.000294
146 ENOG4107U1Q binding-protein-dependent transport systems inner membrane Component -0.000294
146 ENOG4108M2I transcriptional regulator, lysR family -0.000294
146 ENOG4107X07 GntR Family Transcriptional Regulator -0.000294
147 ENOG4105NS2 LysR family transcriptional regulator -0.005578
148 ENOG4108WSZ paraquat-inducible protein a 0.005574
149 ENOG4105WHU Plasmid stabilization system 0.005567
150 ENOG4105VTS DnaJ-like, subfamily C 0.005560
151 ENOG4106H6R UPF0380 protein 0.005557
152 ENOG4108RTX Nitroreductase -0.005546
153 ENOG4108UUM single-stranded DNA-binding protein -0.005541
154 ENOG4107XEC aspartate racemase -0.005537
155 ENOG4105C2E TIM-barrel signal transduction protein -0.000922
155 ENOG4105S10 periplasmic binding protein -0.000922
155 ENOG4108QMA Transcriptional regulator -0.000922
155 ENOG4108UUE Transcriptional regulator -0.000922
155 ENOG4105EQN UPF0261 protein -0.000922
155 ENOG4108VJC ABC transporter, periplasmic molybdate-binding protein -0.000922
156 ENOG4105Q0I thermostable hemolysin -0.005500
157 ENOG4107RNH Outer membrane receptor FepA -0.005484
158 ENOG4107XTP (EAL) domain protein -0.005457
159 ENOG4105ED6 mmge prpd family protein -0.005452
160 ENOG4108VBB NA 0.002724
160 ENOG4106URW exported protein 0.002724
161 ENOG4106N5P YopJ Serine/Threonine acetyltransferase 0.005445
162 ENOG4106G3Z acyl-Coa dehydrogenase -0.005405